It's just barely possible that some idiot decided that the American people could not be told that the airliner had to be shot down and therefore decided to cover it up. But Bush just said again only yesterday that it was an "easy" decision for him to make to give the order to shoot down any plane that threatened to crash into a city or similar target. People would have understood it if that's what happened with Flight 93. The judgment would have been that it was tragic but necessary. After all, everyone in the plane still would have died if it was allowed to crash into the Capitol or the White House.
Bush is no clinton, who lied from instinct, but it's possible that the clintonoid mindset was still lingering in his administration or at the airbase in question, and once they denied there was a shootdown they were stuck with that story.
Still, there's nothing here to confirm it.
I've been underneath a Blue Angel at full boggie that routinely flew 50 to 100' over my house during the Seattle Seafair shows. It mad a small pine tree that was below the level of my head in my neighbors yard shake from the sound. The best I can describe the sound was like the sound of a sheet being ripped amplified about 100,000 times. It physically hurt your heavy organs!
An F-16 probably wasn't what she "didn't" hear, if it was anything at all!!